NEST 2.16.0
WARNING: This version of NEST is affected by issue #1394, which can lead to incorrect simulation results under certain circumstances. Please double-check all simulation results obtained with this version and if in doubt, re-run using a different split between MPI processes and threads. The description of the issue contains more details and will be updated when new information becomes available.
NEST 2.16.0 is the result of 89 merged pull requests by 39 developers since NEST 2.14.0 which was released on 20th of October 2017.
This release contains many bug fixes and improvements. Most notably it brings a new infrastructure for the storage of connections, which reduces the memory consumption and network build times (Jordan et al., 2018).
and extends the rate model framework for novel use-cases (Senden et al., 2018).
Enhancements
Models
- #492: Erfc neuron model
- #671: Adding inhomogeneous poisson generator model
- #845: Allow rectangular and box masks to be rotated
- #849: Aeif psc delta 2 continued
- #858: Extended rate-model framework
- #895: New neuronal population model gif_pop_psc_exp
- #901: Add iaf_psc_exp_ps_lossless model by Krishnan et al
- #966: Fix #825: Improve sign check
- #980: Added parameter to get/set function in tanh_rate model
Installation
- #789: Major change in the installation and testing of packages using multiple python versions
- #890: Add 'install-nodoc' target for make
- #1008: Do not use the -Wall option on K computer
Documentation
Kernel
- #812: Record conductance from aeif_cond_beta_multisynapse model
- #823: Add gamma kernel in topology
- #836: Allow negative exponential distributions (fixes #835)
- #920: NEST 5g simulation kernel
Infrastructure
PyNEST
Fixed Bugs
Models
- #846: Fixes for the gif multisynapse and quantal_stp model
- #860: Fix for #859: Added setting of wfr parameter
- #886: Fix copy/paste bug in copy constructor of Archiving_Node
- #944: Better documentation of hh_cond_exp_traub and Brette-2007-compatible refractory time
- #978: keep conductance positive in gif_cond_exp model
Installation
- #870: Bug fixed on cmake with user modules
- #871: Fixing issue on linking user module libraries with recent GCC versions
- #897: Update NEST Homebrew installation instructions to changes in Homebrew…
- #915: Fix issue 830 - Make fails with UnicodeDecodeError
- #953: Update help generation for MyModule and fix Py27-unicode
Documentation
Kernel
- #840: Fix handling of PyNEST and SLI commandline arguments
- #887: Fix incorrect error message when connecting with bad delay
- #903: Support linking against topology when building extension modules
- #924: Numerical imprecision stdp
- #963: Fixed a bug in the SecondaryEvent delivery
- #1003: Resize Connector vectors when adding connection models
Infrastructure
- #857: Improve handling of output vars from FindXXX.cmake
- #905: Bump version requirement for CMake to support all features, we actually use
- #917: cmake -Dwith-ltdl= fix
- #983: fixed function invocation in hpc_benchmark.py script
- #984: run nosetests with the Python interpreter (2 vs. 3) that was requeste…
PyNEST
- #840: Fix handling of PyNEST and SLI commandline arguments
- #864: Fix test_disconnect by converting filter object to list for len
- #900: Fix Python3 print problem in some tests.
- #947: Remove assertion that argv[0] is a non-empty string in slistartup
Maintenance
Models
- #995: fixed minor issue in WeightRecorderEvent
- #998: Shuts off the warnings from LLVM/Clang 4.0.0
- #1007: Clean up modification of dynamic recordables map in models
Installation
Interpreter
- #948: Obtain help pager information via SLI and handle failures better
- #976: Fix SLI sleep function (fixes #973)
Documentation
- #852: Adapt tarball name in documentation to GitHub convention
- #855: Correct a few typos in documentation comments
- #878: Remove outdated information and redirect to NESTML
- #885: Reinstating code snippets in the Topology User Manual
- #891: Updating import instructions for scipy, sklearn - issue #848
- #912: Fixed doc in GetDefaults
- #913: Return help text
- #927: Documentation of inhomogeneous_poisson_generator
- #930: Updated Topology User Manual for NEST 2.16.
- #943: Added warning against bad use of Rank()
- #950: Fix typo for Hodgkin-Huxley model
- #964: Nest developer space: Description for conversion to 5g
- #965: Fix #949: NEST help files (hlp, html) should end with newline
- #987: README: minor typographic
- #1004: Fix compatibility issues with Python 2
Kernel
- #850: Make Connector properties and growth factor configurable
- #856: Improved structure of secondary event types
- #888: Issue error message when attempting to set an invalid resolution
- #898: Make sure that Run and Cleanup are called after Prepare
- #935: Fix typo in SimulationManager status output
- #956: Fix #954: Avoid the use of unrelated typenames to distinguish template classes
- #962: Improve documentation on setting extent and center (addresses #961)
- #993: Fix 990 / Compilation issues with C++11 and libc++
- #999: Adjust send_recv_count_target_data_
- #1000: Removing pointless comparison with uint
Infrastructure
- #807: Run tests in test_connect_all_patterns.py with mpirun
- #829: Correction in the test of synapse disconnection with mpi
- #884: Updated to VERA++ 1.3.0 in Travis and changed files to comply with style checks
- #909: Reformat and clean up Name definitions
- #914: Fix issue #911
- #928: Fixed issue in help
- #929: Added test for spatial kernels in topology (depends on #823).
- #951: Update platform specific CMake file so it can be used with CMake 3.11.1
- #985: Repo cleanup
- #997: Fix version display during startup
- #1005: Mark more skipped SLI tests as skipped, not success
PyNEST
Contributors since NEST 2.14.0
- Alberto Antonietti
- Rajalekshmi Deepu
- Moritz Deger
- Sandra Diaz
- Jochen Martin Eppler
- Jesús Garrido
- Steffen Graber
- Espen Hagen
- Jan Hahne
- Tammo Ippen
- Jakob Jordan
- Chrisitan Keup
- Itaru Kitayama
- Jeyashree Krishnan
- Tobias Kühn
- Susanne Kunkel
- Mikkel Elle Lepperød
- Charl Linssen
- Jessica Mitchell
- Håkon Mørk
- Abigail Morrison
- Yannick Nodem
- Luciano Paz
- Alexander Peyser
- Hans Ekkehard Plesser
- Jari Pronold
- Luis Riquelme
- Dimitri Rodarie
- Maximilian Schmidt
- Jannis Schuecker
- Mario Senden
- Alex Serenko
- Alexey Shusharin
- Ankur Sinha
- Sebastian Spreizer
- Dennis Terhorst
- Stine Brekke Vennemo
- Philipp Weidel
- Barna Zajzon
Citation
If you use this version of NEST, please cite it as Linssen, Charl et al. (2018). NEST 2.16.0. Zenodo. 10.5281/zenodo.1400175. The full citation is available in different formats on Zenodo.